Antigen

Antigen Class

TFs and others

Antigen

HIF1A

Cell type

Cell type Class

Bone

Cell type

U2OS

Tissue

bone

Lineage

mesoderm

Description

osteosarcoma from the tibia of a 15 year old, J. Ponten and E. Saksela derived this line (originally 2T) in 1964 from a moderately differentiated sarcoma, viruses were not detected during co-cultivation with WI-38 cells or in CF tests against SV40, RSV or adenoviruses, mycoplasma contamination was detected and eliminated in 1972, (PMID: 6081590)

Sample

source_name

U2OS cells

strain

ATCC HTB-96

tissue

bone

genotype

cry1, cry2 double knockout

chip antibody

active motif (cat # 39665).

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

NEXTflex ChIP-seq Kit, Bioo Scientific for chip-seq ChIP-seq procedure as previously described (Cell. 2013 May 9;153(4):855-68). For the Bmal1 and IgG ChIP-seq, the RIPA buffer was diluted 1 to 10. For HIF1A CHIP-seq, protocols are used as described (ChIP-IT high sensitive kit (Cat# 53040, Active Motif)). The library was constructed using a commercially available kit (NEXTflex ChIP-seq Kit, Bioo Scientific). Samples were indexed using NEXTflex™ DNA Barcodes (Bioo Scientific). The library was qualified using an Agilent 2100 Bioanalyzer (Agilent) and quantified using KAPA Library Quantification Kits (Kappa Biosystems). Finally, the indexed libraries were sequenced using a HiSeq 2500 (Illumina).

Sequencing Platform

instrument_model

Illumina HiSeq 2500

hg38

Number of total reads

46980674

Reads aligned (%)

98.0

Duplicates removed (%)

25.1

Number of peaks

16117 (qval < 1E-05)

hg19

Number of total reads

46980674

Reads aligned (%)

97.8

Duplicates removed (%)

25.5

Number of peaks

16177 (qval < 1E-05)